# Analysis of clustering results in conjunction with annotation data.

## Documentation for package `goCluster' version 1.0.3

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

B C D E G H M O P R S

## -- B --

benomylsetup | A test dataset for goCluster
benomylsetupsmall | A test dataset for goCluster

## -- C --

checkannotationpackage | Check if an annotation package contains the specified environment.
checkchrannotation | Check if an annotation package contains the specified environment.
checkData | Checks if a variable contains data.
checkgoannotation | Check if an annotation package contains the specified environment.
checkProtection | A function to protect intermediate results from being overwritten
clusterAlgorithm-class | Class "clusterAlgorithm"
clusterAlgorithmClara-class | Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
clusterAlgorithmHclust-class | Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
clusterAlgorithmKmeans-class | Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
clusterAlgorithmPam-class | Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
clusterAnnotation-class | Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
clusterAnnotationChromosome-abp-class | Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
clusterAnnotationGO-abp-class | Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
clusterclara | Clusters a dataset with the clara function
clusterData-class | Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
clusterhclust | Clusters a dataset using hierarchical clustering
clusterkmeans | Clusters a dataset with the kmeans function
clusterModule-class | Class "clusterModule" represents the base class for all goCluster objects
clusterpam | Clusters a dataset with the pam function
clusterSignif-class | Class "clusterSignif"
clusterSignifBase-class | Class "clusterSignifBase"
clusterSignifBonferroni-class | Class "clusterSignifBonferroni"
clusterSignifFDR-class | Class "clusterSignifFDR"
clusterStatistic-class | Class "clusterStatistic" provides statistical analysis for goCluster
clusterStatisticHyper-class | Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
clusterVisual-class | Class "clusterVisual"
clusterVisualHclust-class | Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
clusterVisualHeatmap-class | Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
clusterVisualNone-class | Class "clusterVisualNone", a placeholder for the goCluster visualization methods
collectTerms | A function to collect all annotation terms of a tree
config | Interactively configure a goCluster-module
config,clusterAlgorithm-method | Class "clusterAlgorithm"
config,clusterAlgorithmClara-method | Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
config,clusterAlgorithmHclust-method | Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
config,clusterAlgorithmKmeans-method | Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
config,clusterAlgorithmPam-method | Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
config,clusterAnnotation-method | Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
config,clusterAnnotationChromosome-abp-method | Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
config,clusterAnnotationGO-abp-method | Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
config,clusterData-method | Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
config,clusterModule-method | Class "clusterModule" represents the base class for all goCluster objects
config,clusterSignif-method | Class "clusterSignif"
config,clusterSignifBase-method | Class "clusterSignifBase"
config,clusterSignifBonferroni-method | Class "clusterSignifBonferroni"
config,clusterSignifFDR-method | Class "clusterSignifFDR"
config,clusterStatistic-method | Class "clusterStatistic" provides statistical analysis for goCluster
config,clusterStatisticHyper-method | Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
config,clusterVisual-method | Class "clusterVisual"
config,clusterVisualHclust-method | Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
config,clusterVisualHeatmap-method | Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
config,clusterVisualNone-method | Class "clusterVisualNone", a placeholder for the goCluster visualization methods
config,goCluster-method | Class "goCluster", a class for combining clustering results with functional annotation

## -- D --

display | Display a visualization module
display,clusterVisual-method | Class "clusterVisual"
display,clusterVisualHclust-method | Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
display,clusterVisualHeatmap-method | Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
display,clusterVisualNone-method | Class "clusterVisualNone", a placeholder for the goCluster visualization methods
display,goCluster-method | Class "goCluster", a class for combining clustering results with functional annotation

## -- E --

evalAnnosetHyper | Evaluates a clustering result with regard to an enrichment of annotation terms in specific clusters.
evalClusterHyper | Evaluates a clustering result with regard to an enrichment of annotation terms in specific clusters.
EVIDENCECODES | Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
execute | Executes a goCluster-module
execute,clusterAlgorithm-method | Class "clusterAlgorithm"
execute,clusterAlgorithmClara-method | Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
execute,clusterAlgorithmHclust-method | Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
execute,clusterAlgorithmKmeans-method | Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
execute,clusterAlgorithmPam-method | Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
execute,clusterAnnotation-method | Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
execute,clusterAnnotationChromosome-abp-method | Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
execute,clusterAnnotationGO-abp-method | Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
execute,clusterData-method | Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
execute,clusterModule-method | Class "clusterModule" represents the base class for all goCluster objects
execute,clusterSignif-method | Class "clusterSignif"
execute,clusterSignifBase-method | Class "clusterSignifBase"
execute,clusterSignifBonferroni-method | Class "clusterSignifBonferroni"
execute,clusterSignifFDR-method | Class "clusterSignifFDR"
execute,clusterStatistic-method | Class "clusterStatistic" provides statistical analysis for goCluster
execute,clusterStatisticHyper-method | Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
execute,clusterVisual-method | Class "clusterVisual"
execute,clusterVisualHclust-method | Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
execute,clusterVisualHeatmap-method | Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
execute,clusterVisualNone-method | Class "clusterVisualNone", a placeholder for the goCluster visualization methods
execute<-,clusterModule-method | Class "clusterModule" represents the base class for all goCluster objects

## -- G --

getChildrenClasses | Get the children of an abstract class
getGeneColors | Returns a set of colors
goCluster-class | Class "goCluster", a class for combining clustering results with functional annotation
goClusterTk | Class "goCluster", a class for combining clustering results with functional annotation
groupCount | Count the number of clusters

## -- H --

HCLUSTDISTANCE | Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
HCLUSTMETHOD | Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.

## -- M --

mergeAnno | Select interesting annotation terms after FDR analysis
mergeResult | Merges two lists of selected genes to the selection with minimal p-value
minimizeSelection | Reduces the leaves of a tree to minimal p-values

## -- O --

ONTOLOGIES | Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.

## -- P --

plotAxis | Plots the axis besides a hierarchical clustering
prepareAxis | Reduces a tree of selected items to a vector of non-overelapping regions with minimal p-value
prepareCHRannotation | A function to prepare the gene localization for subsequent statistical analysis
prepareGOannotation | A function to prepare the gene ontology annotation for subsequent statistical analysis
prepareHeatmap | A function to reformat a goCluster result for graphical representation
print,clusterAlgorithm-method | Class "clusterAlgorithm"
print,clusterAlgorithmClara-method | Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
print,clusterAlgorithmHclust-method | Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
print,clusterAlgorithmKmeans-method | Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
print,clusterAlgorithmPam-method | Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
print,clusterAnnotation-method | Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
print,clusterAnnotationChromosome-abp-method | Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
print,clusterAnnotationGO-abp-method | Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
print,clusterData-method | Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
print,clusterSignif-method | Class "clusterSignif"
print,clusterSignifBase-method | Class "clusterSignifBase"
print,clusterSignifBonferroni-method | Class "clusterSignifBonferroni"
print,clusterSignifFDR-method | Class "clusterSignifFDR"
print,clusterStatistic-method | Class "clusterStatistic" provides statistical analysis for goCluster
print,clusterStatisticHyper-method | Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
print,clusterVisual-method | Class "clusterVisual"
print,clusterVisualHclust-method | Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
print,clusterVisualHeatmap-method | Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
print,clusterVisualNone-method | Class "clusterVisualNone", a placeholder for the goCluster visualization methods
print,goCluster-method | Class "goCluster", a class for combining clustering results with functional annotation
printData | Helper printing function

## -- R --

randomizeTree | Select interesting annotation terms after FDR analysis
reset | Reset a goCluster-module
reset,clusterAlgorithm-method | Class "clusterAlgorithm"
reset,clusterAlgorithmClara-method | Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
reset,clusterAlgorithmHclust-method | Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
reset,clusterAlgorithmKmeans-method | Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
reset,clusterAlgorithmPam-method | Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
reset,clusterAnnotation-method | Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
reset,clusterAnnotationChromosome-abp-method | Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
reset,clusterAnnotationGO-abp-method | Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
reset,clusterData-method | Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
reset,clusterModule-method | Class "clusterModule" represents the base class for all goCluster objects
reset,clusterSignif-method | Class "clusterSignif"
reset,clusterSignifBase-method | Class "clusterSignifBase"
reset,clusterSignifBonferroni-method | Class "clusterSignifBonferroni"
reset,clusterSignifFDR-method | Class "clusterSignifFDR"
reset,clusterStatistic-method | Class "clusterStatistic" provides statistical analysis for goCluster
reset,clusterStatisticHyper-method | Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
reset,clusterVisual-method | Class "clusterVisual"
reset,clusterVisualHclust-method | Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
reset,clusterVisualHeatmap-method | Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
reset,clusterVisualNone-method | Class "clusterVisualNone", a placeholder for the goCluster visualization methods
reset,goCluster-method | Class "goCluster", a class for combining clustering results with functional annotation
run,goCluster-method | Class "goCluster", a class for combining clustering results with functional annotation
run<-,goCluster-method | Class "goCluster", a class for combining clustering results with functional annotation

## -- S --

selectAnnoStats | Select interesting annotation terms after FDR analysis
selectChild | Choosing the child of an abstract class
selectCore | A menu function
selectCorePlain | A menu function
selectCoreTk | A menu function
selectDouble | A menu for choosing a floating point number
selectNumber | A menu for choosing an integer
selectOption | A menu for choosing an option
selectOptions | A menu for choosing an option
selectStats | Selects relevant annotation terms
selectStatsBonferroni | Performs Bonferroni correction and subsequently selects relevant annotation terms.
selectTerms | A function to select interesting annotation terms with the associated genes from a goCluster object
setup | Returns the setup of a goCluster-module
setup,clusterAlgorithm-method | Class "clusterAlgorithm"
setup,clusterAlgorithmClara-method | Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
setup,clusterAlgorithmHclust-method | Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
setup,clusterAlgorithmKmeans-method | Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
setup,clusterAlgorithmPam-method | Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
setup,clusterAnnotation-method | Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
setup,clusterAnnotationChromosome-abp-method | Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
setup,clusterAnnotationGO-abp-method | Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
setup,clusterData-method | Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
setup,clusterModule-method | Class "clusterModule" represents the base class for all goCluster objects
setup,clusterSignif-method | Class "clusterSignif"
setup,clusterSignifBase-method | Class "clusterSignifBase"
setup,clusterSignifBonferroni-method | Class "clusterSignifBonferroni"
setup,clusterSignifFDR-method | Class "clusterSignifFDR"
setup,clusterStatistic-method | Class "clusterStatistic" provides statistical analysis for goCluster
setup,clusterStatisticHyper-method | Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
setup,clusterVisual-method | Class "clusterVisual"
setup,clusterVisualHclust-method | Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
setup,clusterVisualHeatmap-method | Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
setup,clusterVisualNone-method | Class "clusterVisualNone", a placeholder for the goCluster visualization methods
setup,goCluster-method | Class "goCluster", a class for combining clustering results with functional annotation
setup<-,clusterAlgorithm-method | Class "clusterAlgorithm"
setup<-,clusterAlgorithmClara-method | Class "clusterAlgorithmClara", provides partitioning around medoids of large datasets
setup<-,clusterAlgorithmHclust-method | Class "clusterAlgorithmHclust", provides hierarchical clustering for goCluster.
setup<-,clusterAlgorithmKmeans-method | Class "clusterAlgorithmKmeans", provides kmeans clustering for goCluster.
setup<-,clusterAlgorithmPam-method | Class "clusterAlgorithmPam", provides partitioning around medoids for goCluster.
setup<-,clusterAnnotation-method | Class "clusterAnnotation", an abstract class that represents functions for annotating microarray datasets.
setup<-,clusterAnnotationChromosome-abp-method | Class "clusterAnnotationChromosome-abp", prepares the chromosome annotation for subsequent statistical analysis.
setup<-,clusterAnnotationGO-abp-method | Class "clusterAnnotationGO-abp", prepares the GO annotation for subsequent statistical analysis.
setup<-,clusterData-method | Class "clusterData", a class for holding datasets that are going to be analysed with goCluster.
setup<-,clusterModule-method | Class "clusterModule" represents the base class for all goCluster objects
setup<-,clusterSignif-method | Class "clusterSignif"
setup<-,clusterSignifBase-method | Class "clusterSignifBase"
setup<-,clusterSignifBonferroni-method | Class "clusterSignifBonferroni"
setup<-,clusterSignifFDR-method | Class "clusterSignifFDR"
setup<-,clusterStatistic-method | Class "clusterStatistic" provides statistical analysis for goCluster
setup<-,clusterStatisticHyper-method | Class "clusterStatisticHyper" provides the hypergeometric distribution for the goCluster analysis.
setup<-,clusterVisual-method | Class "clusterVisual"
setup<-,clusterVisualHclust-method | Class "clusterVisualHclust" prepares a visualization for a dataset that has been clustered with hierarchical clustering.
setup<-,clusterVisualHeatmap-method | Class "clusterVisualHeatmap", prepares a goCluster analysis for visualization.
setup<-,clusterVisualNone-method | Class "clusterVisualNone", a placeholder for the goCluster visualization methods
setup<-,goCluster-method | Class "goCluster", a class for combining clustering results with functional annotation